Hi,
First, I didn't mention this before but you had mentioned you're using
Amber 12. I highly recommend you use cpptraj from AmberTools 14 for
analysis (
http://ambermd.org/AmberTools14-get.html).
Second, it's not clear what input you are using when you do not get
your stripped topology. In general when you have an issue with cpptraj
it's best to post *exactly* what you ran: command and all lines of
input. Otherwise we have to guess at what's going wrong which is
usually not productive.
Based on the input you provided before and the recommendations I made,
you should be running something like this:
parm 1blb_dimer.prmtop
trajin 1blb_dimer-prod-1.mdcrd 1 50 1
strip :WAT,Na+ outprefix strip
trajout strip.md.nc netcdf
This should produce 'strip.1blb_dimer.prmtop' which is your stripped
topology file and 'strip.md.nc' which is your stripped trajectory
file. Were either of these files not generated? Or did you perhaps use
different input?
-Dan
On Wed, Jan 7, 2015 at 1:33 PM, Ibrahim Said <saidibrahim569.gmail.com> wrote:
> Dear Dan
> This is the first error I have faced. cpptraj can not write this
> strip.1blb_dimer.prmtop.
>
> said
>
> On Wed, Jan 7, 2015 at 10:26 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Sorry, you need to use the stripped topology of course:
>>
>> > parm 1blb_dimer.prmtop
>>
>> should instead be
>>
>> parm strip.1blb_dimer.prmtop
>>
>> which should have been generated in the previous step.
>>
>> -Dan
>>
>> > trajin strip.md.nc
>> > rms :1-185 first
>> > average chain1.pdb :1-185 pdb
>> > rms :186-366 first
>> > average chain2.pdb :186-366 pdb
>> >
>> > -Dan
>> >
>> > On Wed, Jan 7, 2015 at 12:39 PM, Ibrahim Said <saidibrahim569.gmail.com>
>> wrote:
>> >> Dear Dan
>> >> My full script is
>> >> parm 1blb_dimer.prmtop
>> >> trajin 1blb_dimer-prod-1.mdcrd 1 50 1
>> >> -
>> >> -
>> >> -
>> >> strip :WAT
>> >> strip :Na+
>> >> average chain1.pdb :1-185 pdb
>> >> average chain2.pdb :186-366 pdb
>> >> trajout strip.md.nc netcdf
>> >> Also I did not see the previous massage.
>> >>
>> >> said
>> >>
>> >> On Wed, Jan 7, 2015 at 9:33 PM, David A Case <case.biomaps.rutgers.edu>
>> >> wrote:
>> >>
>> >>> On Wed, Jan 07, 2015, Ibrahim Said wrote:
>> >>>
>> >>> > I added the line parm protein.prmtop, but I did not get
>> >>> > strip.protein.prmtop.
>> >>>
>> >>> This sounds like progress, assuming that all the other error messages
>> >>> (relating to not being able to open the protein.prmtop file) are gone.
>> >>>
>> >>> > > > trajin 1blb_dimer-prod-1.mdcrd 1 50 1
>> >>> > > > -
>> >>> > > > -
>> >>> > > > -
>> >>> > > > trajin 1blb_dimer-prod-12.mdcrd 1 100 1
>> >>> > > > trajout strip.md.nc netcdf
>> >>>
>> >>> The above script doesn't have any "strip" commands in it. Are you
>> actually
>> >>> expecting to strip atoms?
>> >>>
>> >>> If you want to get a stripped prmtop file (in addition to a stripped
>> >>> trajectory file), you need to have a "strip" line with the "outprefix"
>> >>> option.
>> >>> (And if you just want to combine several trajectory files into a single
>> >>> one,
>> >>> without stripping atoms, then there is no need to create a new prmtop
>> >>> file.)
>> >>>
>> >>> ...hope this helps...dac
>> >>>
>> >>>
>> >>> _______________________________________________
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>> >>>
>> >> _______________________________________________
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>> >
>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 307
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jan 07 2015 - 14:00:07 PST
